from __future__ import absolute_import, division, print_function from scitbx.array_family import flex from libtbx import group_args from libtbx.utils import user_plus_sys_time from mmtbx.refinement.real_space import individual_sites import mmtbx from six.moves import range pdb_str_answer = """\ CRYST1 23.136 23.980 28.180 90.00 90.00 90.00 P 1 ATOM 1 O5' DC A 1 18.769 14.782 4.393 1.00 6.75 O ATOM 2 C5' DC A 1 19.006 13.768 5.373 1.00 5.76 C ATOM 3 C4' DC A 1 17.877 12.780 5.508 1.00 5.43 C ATOM 4 O4' DC A 1 16.718 13.456 6.038 1.00 6.23 O ATOM 5 C3' DC A 1 17.408 12.109 4.197 1.00 5.76 C ATOM 6 O3' DC A 1 17.067 10.753 4.414 1.00 6.24 O ATOM 7 C2' DC A 1 16.176 12.865 3.829 1.00 5.97 C ATOM 8 C1' DC A 1 15.604 13.235 5.204 1.00 5.80 C ATOM 9 N1 DC A 1 14.782 14.462 5.186 1.00 5.86 N ATOM 10 C2 DC A 1 13.418 14.369 4.997 1.00 5.95 C ATOM 11 O2 DC A 1 12.899 13.225 4.851 1.00 7.16 O ATOM 12 N3 DC A 1 12.644 15.476 4.959 1.00 5.87 N ATOM 13 C4 DC A 1 13.230 16.686 5.118 1.00 5.87 C ATOM 14 N4 DC A 1 12.439 17.760 5.083 1.00 6.52 N ATOM 15 C5 DC A 1 14.638 16.833 5.308 1.00 6.61 C ATOM 16 C6 DC A 1 15.363 15.687 5.329 1.00 6.96 C ATOM 17 P DG A 2 18.103 9.542 4.276 1.00 6.42 P ATOM 18 OP1 DG A 2 19.079 9.771 3.150 1.00 7.41 O ATOM 19 OP2 DG A 2 17.248 8.315 4.226 1.00 7.63 O ATOM 20 O5' DG A 2 18.994 9.571 5.600 1.00 6.87 O ATOM 21 C5' DG A 2 18.415 9.369 6.879 1.00 6.28 C ATOM 22 C4' DG A 2 19.448 9.733 7.953 1.00 6.57 C ATOM 23 O4' DG A 2 19.856 11.086 7.791 1.00 6.18 O ATOM 24 C3' DG A 2 18.941 9.610 9.402 1.00 6.90 C ATOM 25 O3' DG A 2 19.154 8.270 9.879 1.00 8.35 O ATOM 26 C2' DG A 2 19.700 10.666 10.139 1.00 7.77 C ATOM 27 C1' DG A 2 20.136 11.660 9.131 1.00 6.65 C ATOM 28 N9 DG A 2 19.464 12.952 9.099 1.00 6.28 N ATOM 29 C8 DG A 2 20.053 14.194 9.112 1.00 7.19 C ATOM 30 N7 DG A 2 19.229 15.185 9.059 1.00 7.47 N ATOM 31 C5 DG A 2 17.967 14.561 8.992 1.00 5.84 C ATOM 32 C6 DG A 2 16.667 15.118 8.902 1.00 5.59 C ATOM 33 O6 DG A 2 16.345 16.344 8.881 1.00 6.73 O ATOM 34 N1 DG A 2 15.678 14.152 8.859 1.00 5.14 N ATOM 35 C2 DG A 2 15.918 12.799 8.880 1.00 4.97 C ATOM 36 N2 DG A 2 14.843 12.012 8.812 1.00 5.85 N ATOM 37 N3 DG A 2 17.133 12.263 8.960 1.00 5.27 N ATOM 38 C4 DG A 2 18.094 13.192 9.015 1.00 5.60 C ATOM 39 P DC A 3 17.905 7.353 10.333 1.00 8.32 P ATOM 40 OP1 DC A 3 18.531 6.058 10.697 1.00 10.45 O ATOM 41 OP2 DC A 3 16.864 7.362 9.303 1.00 9.29 O ATOM 42 O5' DC A 3 17.434 8.114 11.651 1.00 7.83 O ATOM 43 C5' DC A 3 16.856 7.412 12.761 1.00 6.84 C ATOM 44 C4' DC A 3 15.465 7.945 13.113 1.00 6.76 C ATOM 45 O4' DC A 3 15.564 9.296 13.572 1.00 6.82 O ATOM 46 C3' DC A 3 14.464 7.959 11.956 1.00 7.23 C ATOM 47 O3' DC A 3 13.169 7.697 12.441 1.00 8.29 O ATOM 48 C2' DC A 3 14.478 9.374 11.464 1.00 7.01 C ATOM 49 C1' DC A 3 14.673 10.096 12.792 1.00 6.65 C ATOM 50 N1 DC A 3 15.294 11.429 12.660 1.00 6.27 N ATOM 51 C2 DC A 3 14.431 12.528 12.451 1.00 6.39 C ATOM 52 O2 DC A 3 13.224 12.349 12.410 1.00 6.84 O ATOM 53 N3 DC A 3 15.018 13.772 12.326 1.00 6.04 N ATOM 54 C4 DC A 3 16.331 13.903 12.377 1.00 6.43 C ATOM 55 N4 DC A 3 16.826 15.147 12.241 1.00 7.42 N ATOM 56 C5 DC A 3 17.207 12.775 12.563 1.00 7.12 C ATOM 57 C6 DC A 3 16.622 11.579 12.698 1.00 6.73 C ATOM 58 P DG A 4 12.497 6.227 12.392 1.00 9.26 P ATOM 59 OP1 DG A 4 12.848 5.570 11.074 1.00 12.46 O ATOM 60 OP2 DG A 4 11.080 6.441 12.826 1.00 14.73 O ATOM 61 O5' DG A 4 13.267 5.407 13.510 1.00 7.56 O ATOM 62 C5' DG A 4 13.061 5.684 14.893 1.00 6.32 C ATOM 63 C4' DG A 4 14.029 4.913 15.745 1.00 5.92 C ATOM 64 O4' DG A 4 15.366 5.301 15.383 1.00 5.78 O ATOM 65 C3' DG A 4 13.916 5.172 17.257 1.00 5.01 C ATOM 66 O3' DG A 4 12.999 4.199 17.771 1.00 5.69 O ATOM 67 C2' DG A 4 15.325 5.056 17.776 1.00 6.12 C ATOM 68 C1' DG A 4 16.228 5.340 16.601 1.00 5.65 C ATOM 69 N9 DG A 4 16.915 6.618 16.530 1.00 5.85 N ATOM 70 C8 DG A 4 18.291 6.782 16.475 1.00 7.25 C ATOM 71 N7 DG A 4 18.680 8.017 16.413 1.00 7.01 N ATOM 72 C5 DG A 4 17.464 8.741 16.415 1.00 5.60 C ATOM 73 C6 DG A 4 17.242 10.148 16.359 1.00 5.58 C ATOM 74 O6 DG A 4 18.121 11.031 16.291 1.00 6.97 O ATOM 75 N1 DG A 4 15.891 10.462 16.389 1.00 5.26 N ATOM 76 C2 DG A 4 14.889 9.555 16.456 1.00 4.93 C ATOM 77 N2 DG A 4 13.638 10.069 16.465 1.00 5.47 N ATOM 78 N3 DG A 4 15.072 8.221 16.519 1.00 5.01 N ATOM 79 C4 DG A 4 16.385 7.910 16.495 1.00 5.12 C ATOM 80 P DC A 5 12.572 4.152 19.322 1.00 5.45 P ATOM 81 OP1 DC A 5 13.736 4.126 20.235 1.00 7.21 O ATOM 82 OP2 DC A 5 11.598 3.000 19.416 1.00 6.66 O ATOM 83 O5' DC A 5 11.791 5.543 19.444 1.00 5.28 O ATOM 84 C5' DC A 5 10.979 5.787 20.626 1.00 4.67 C ATOM 85 C4' DC A 5 10.589 7.248 20.660 1.00 4.60 C ATOM 86 O4' DC A 5 11.727 8.033 21.072 1.00 4.74 O ATOM 87 C3' DC A 5 10.101 7.836 19.317 1.00 4.77 C ATOM 88 O3' DC A 5 9.017 8.722 19.505 1.00 5.08 O ATOM 89 C2' DC A 5 11.292 8.621 18.827 1.00 4.62 C ATOM 90 C1' DC A 5 11.958 9.078 20.121 1.00 4.39 C ATOM 91 N1 DC A 5 13.411 9.260 20.041 1.00 4.58 N ATOM 92 C2 DC A 5 13.939 10.568 19.863 1.00 4.24 C ATOM 93 O2 DC A 5 13.163 11.535 19.786 1.00 4.74 O ATOM 94 N3 DC A 5 15.298 10.717 19.786 1.00 4.45 N ATOM 95 C4 DC A 5 16.094 9.653 19.871 1.00 4.35 C ATOM 96 N4 DC A 5 17.408 9.835 19.801 1.00 5.02 N ATOM 97 C5 DC A 5 15.570 8.322 20.058 1.00 5.31 C ATOM 98 C6 DC A 5 14.243 8.187 20.118 1.00 4.82 C ATOM 99 P DG A 6 7.494 8.228 19.402 1.00 5.08 P ATOM 100 OP1 DG A 6 7.310 7.262 18.277 1.00 6.02 O ATOM 101 OP2 DG A 6 6.660 9.486 19.429 1.00 6.23 O ATOM 102 O5' DG A 6 7.212 7.367 20.738 1.00 5.07 O ATOM 103 C5' DG A 6 7.051 7.997 22.037 1.00 5.27 C ATOM 104 C4' DG A 6 6.878 6.925 23.088 1.00 5.46 C ATOM 105 O4' DG A 6 8.106 6.152 23.156 1.00 5.73 O ATOM 106 C3' DG A 6 6.580 7.396 24.517 1.00 5.95 C ATOM 107 O3' DG A 6 5.694 6.529 25.180 1.00 6.71 O ATOM 108 C2' DG A 6 7.953 7.365 25.168 1.00 5.78 C ATOM 109 C1' DG A 6 8.598 6.176 24.518 1.00 5.71 C ATOM 110 N9 DG A 6 10.051 6.215 24.426 1.00 5.53 N ATOM 111 C8 DG A 6 10.886 5.131 24.573 1.00 6.04 C ATOM 112 N7 DG A 6 12.120 5.390 24.441 1.00 6.08 N ATOM 113 C5 DG A 6 12.156 6.739 24.175 1.00 5.46 C ATOM 114 C6 DG A 6 13.245 7.610 23.935 1.00 5.43 C ATOM 115 O6 DG A 6 14.472 7.293 23.919 1.00 7.16 O ATOM 116 N1 DG A 6 12.861 8.910 23.717 1.00 4.97 N ATOM 117 C2 DG A 6 11.580 9.343 23.699 1.00 4.93 C ATOM 118 N2 DG A 6 11.374 10.652 23.451 1.00 5.51 N ATOM 119 N3 DG A 6 10.512 8.551 23.926 1.00 5.24 N ATOM 120 C4 DG A 6 10.888 7.269 24.156 1.00 5.04 C TER ATOM 121 O5' DC B 11 18.926 15.402 23.792 1.00 8.02 O ATOM 122 C5' DC B 11 18.416 16.333 22.847 1.00 6.88 C ATOM 123 C4' DC B 11 16.899 16.301 22.748 1.00 5.81 C ATOM 124 O4' DC B 11 16.480 15.034 22.222 1.00 5.58 O ATOM 125 C3' DC B 11 16.099 16.450 24.062 1.00 5.79 C ATOM 126 O3' DC B 11 14.877 17.152 23.896 1.00 5.67 O ATOM 127 C2' DC B 11 15.784 15.014 24.475 1.00 5.97 C ATOM 128 C1' DC B 11 15.580 14.368 23.065 1.00 5.24 C ATOM 129 N1 DC B 11 15.882 12.934 23.082 1.00 5.01 N ATOM 130 C2 DC B 11 14.847 12.021 23.209 1.00 4.82 C ATOM 131 O2 DC B 11 13.666 12.396 23.290 1.00 5.52 O ATOM 132 N3 DC B 11 15.151 10.700 23.262 1.00 4.74 N ATOM 133 C4 DC B 11 16.452 10.300 23.188 1.00 4.81 C ATOM 134 N4 DC B 11 16.692 8.979 23.227 1.00 5.77 N ATOM 135 C5 DC B 11 17.509 11.226 23.042 1.00 5.27 C ATOM 136 C6 DC B 11 17.166 12.534 23.005 1.00 5.27 C ATOM 137 P DG B 12 14.738 18.742 23.923 1.00 5.73 P ATOM 138 OP1 DG B 12 15.560 19.334 25.015 1.00 7.08 O ATOM 139 OP2 DG B 12 13.260 18.999 23.911 1.00 6.80 O ATOM 140 O5' DG B 12 15.384 19.231 22.538 1.00 5.63 O ATOM 141 C5' DG B 12 14.783 18.830 21.263 1.00 5.55 C ATOM 142 C4' DG B 12 15.691 19.270 20.124 1.00 5.48 C ATOM 143 O4' DG B 12 16.967 18.683 20.271 1.00 5.59 O ATOM 144 C3' DG B 12 15.187 18.840 18.742 1.00 5.35 C ATOM 145 O3' DG B 12 14.327 19.843 18.179 1.00 5.75 O ATOM 146 C2' DG B 12 16.450 18.633 17.932 1.00 6.20 C ATOM 147 C1' DG B 12 17.527 18.400 18.932 1.00 5.70 C ATOM 148 N9 DG B 12 18.007 17.025 19.037 1.00 5.43 N ATOM 149 C8 DG B 12 19.344 16.654 19.033 1.00 6.29 C ATOM 150 N7 DG B 12 19.526 15.347 19.161 1.00 6.25 N ATOM 151 C5 DG B 12 18.218 14.827 19.251 1.00 5.07 C ATOM 152 C6 DG B 12 17.785 13.503 19.394 1.00 5.05 C ATOM 153 O6 DG B 12 18.473 12.458 19.472 1.00 6.39 O ATOM 154 N1 DG B 12 16.381 13.433 19.443 1.00 4.49 N ATOM 155 C2 DG B 12 15.529 14.511 19.382 1.00 4.50 C ATOM 156 N2 DG B 12 14.216 14.246 19.458 1.00 5.39 N ATOM 157 N3 DG B 12 15.942 15.754 19.240 1.00 4.99 N ATOM 158 C4 DG B 12 17.303 15.861 19.182 1.00 4.82 C ATOM 159 P DC B 13 12.749 19.626 18.034 1.00 5.23 P ATOM 160 OP1 DC B 13 12.194 20.980 17.701 1.00 6.06 O ATOM 161 OP2 DC B 13 12.186 18.926 19.224 1.00 6.16 O ATOM 162 O5' DC B 13 12.689 18.675 16.744 1.00 6.62 O ATOM 163 C5' DC B 13 11.704 18.813 15.707 1.00 5.76 C ATOM 164 C4' DC B 13 11.117 17.442 15.391 1.00 5.29 C ATOM 165 O4' DC B 13 12.152 16.582 14.797 1.00 5.84 O ATOM 166 C3' DC B 13 10.535 16.656 16.565 1.00 5.51 C ATOM 167 O3' DC B 13 9.392 15.893 16.173 1.00 5.91 O ATOM 168 C2' DC B 13 11.657 15.727 16.940 1.00 6.03 C ATOM 169 C1' DC B 13 12.262 15.400 15.551 1.00 5.71 C ATOM 170 N1 DC B 13 13.686 15.016 15.630 1.00 5.35 N ATOM 171 C2 DC B 13 13.999 13.675 15.839 1.00 5.14 C ATOM 172 O2 DC B 13 13.077 12.844 15.945 1.00 5.75 O ATOM 173 N3 DC B 13 15.315 13.303 15.935 1.00 5.24 N ATOM 174 C4 DC B 13 16.250 14.212 15.820 1.00 5.38 C ATOM 175 N4 DC B 13 17.551 13.848 15.907 1.00 6.48 N ATOM 176 C5 DC B 13 15.980 15.587 15.611 1.00 6.18 C ATOM 177 C6 DC B 13 14.676 15.941 15.515 1.00 5.88 C ATOM 178 P DG B 14 7.907 16.465 16.240 1.00 6.36 P ATOM 179 OP1 DG B 14 7.703 17.278 17.477 1.00 6.92 O ATOM 180 OP2 DG B 14 7.024 15.292 16.034 1.00 8.20 O ATOM 181 O5' DG B 14 7.782 17.484 14.993 1.00 6.06 O ATOM 182 C5' DG B 14 7.865 16.961 13.667 1.00 5.87 C ATOM 183 C4' DG B 14 7.769 18.118 12.661 1.00 5.61 C ATOM 184 O4' DG B 14 8.840 19.044 12.888 1.00 6.39 O ATOM 185 C3' DG B 14 7.848 17.657 11.210 1.00 6.20 C ATOM 186 O3' DG B 14 6.556 17.482 10.636 1.00 6.92 O ATOM 187 C2' DG B 14 8.640 18.776 10.533 1.00 6.66 C ATOM 188 C1' DG B 14 9.397 19.489 11.623 1.00 6.45 C ATOM 189 N9 DG B 14 10.837 19.220 11.720 1.00 5.88 N ATOM 190 C8 DG B 14 11.821 20.181 11.747 1.00 6.66 C ATOM 191 N7 DG B 14 13.033 19.687 11.849 1.00 6.84 N ATOM 192 C5 DG B 14 12.836 18.306 11.888 1.00 5.83 C ATOM 193 C6 DG B 14 13.787 17.273 11.979 1.00 5.83 C ATOM 194 O6 DG B 14 15.032 17.344 12.058 1.00 7.03 O ATOM 195 N1 DG B 14 13.147 16.004 11.973 1.00 5.52 N ATOM 196 C2 DG B 14 11.799 15.795 11.901 1.00 5.22 C ATOM 197 N2 DG B 14 11.395 14.534 11.922 1.00 5.90 N ATOM 198 N3 DG B 14 10.912 16.785 11.810 1.00 5.73 N ATOM 199 C4 DG B 14 11.486 18.002 11.806 1.00 5.44 C ATOM 200 P DC B 15 5.984 16.067 10.203 1.00 7.01 P ATOM 201 OP1 DC B 15 4.596 16.315 9.735 1.00 8.31 O ATOM 202 OP2 DC B 15 6.231 15.081 11.304 1.00 10.11 O ATOM 203 O5' DC B 15 6.895 15.773 8.944 1.00 8.26 O ATOM 204 C5' DC B 15 6.422 15.063 7.798 1.00 6.44 C ATOM 205 C4' DC B 15 7.319 13.882 7.508 1.00 6.19 C ATOM 206 O4' DC B 15 8.617 14.367 7.098 1.00 6.22 O ATOM 207 C3' DC B 15 7.608 12.913 8.672 1.00 6.74 C ATOM 208 O3' DC B 15 7.616 11.558 8.249 1.00 7.06 O ATOM 209 C2' DC B 15 8.977 13.298 9.148 1.00 7.26 C ATOM 210 C1' DC B 15 9.643 13.752 7.880 1.00 6.21 C ATOM 211 N1 DC B 15 10.694 14.769 8.067 1.00 5.66 N ATOM 212 C2 DC B 15 12.004 14.337 8.318 1.00 5.46 C ATOM 213 O2 DC B 15 12.229 13.104 8.348 1.00 6.74 O ATOM 214 N3 DC B 15 12.996 15.236 8.500 1.00 5.33 N ATOM 215 C4 DC B 15 12.695 16.549 8.464 1.00 5.54 C ATOM 216 N4 DC B 15 13.712 17.414 8.637 1.00 6.29 N ATOM 217 C5 DC B 15 11.369 17.030 8.229 1.00 6.28 C ATOM 218 C6 DC B 15 10.424 16.108 8.047 1.00 5.99 C ATOM 219 P DG B 16 6.306 10.627 8.322 1.00 7.56 P ATOM 220 OP1 DG B 16 5.687 10.785 9.659 1.00 9.30 O ATOM 221 OP2 DG B 16 6.749 9.256 7.911 1.00 10.00 O ATOM 222 O5' DG B 16 5.295 11.234 7.254 1.00 6.99 O ATOM 223 C5' DG B 16 5.430 10.976 5.847 1.00 6.54 C ATOM 224 C4' DG B 16 4.379 11.744 5.091 1.00 5.93 C ATOM 225 O4' DG B 16 4.628 13.152 5.234 1.00 5.90 O ATOM 226 C3' DG B 16 4.307 11.492 3.565 1.00 6.25 C ATOM 227 O3' DG B 16 3.000 11.676 3.022 1.00 6.18 O ATOM 228 C2' DG B 16 5.200 12.524 3.000 1.00 6.00 C ATOM 229 C1' DG B 16 4.848 13.731 3.896 1.00 5.55 C ATOM 230 N9 DG B 16 5.827 14.784 4.044 1.00 5.41 N ATOM 231 C8 DG B 16 5.526 16.116 4.101 1.00 5.68 C ATOM 232 N7 DG B 16 6.576 16.892 4.248 1.00 6.51 N ATOM 233 C5 DG B 16 7.648 16.010 4.302 1.00 5.15 C ATOM 234 C6 DG B 16 9.040 16.260 4.456 1.00 5.40 C ATOM 235 O6 DG B 16 9.610 17.365 4.578 1.00 6.71 O ATOM 236 N1 DG B 16 9.781 15.081 4.446 1.00 5.34 N ATOM 237 C2 DG B 16 9.275 13.842 4.341 1.00 4.88 C ATOM 238 N2 DG B 16 10.116 12.805 4.369 1.00 6.11 N ATOM 239 N3 DG B 16 7.959 13.565 4.196 1.00 5.45 N ATOM 240 C4 DG B 16 7.217 14.680 4.179 1.00 5.38 C TER END """ pdb_str_poor = """\ CRYST1 23.136 23.980 28.180 90.00 90.00 90.00 P 1 ATOM 1 O5' DC A 1 18.558 14.341 2.992 1.00 6.75 O ATOM 2 C5' DC A 1 19.062 13.253 4.169 1.00 5.76 C ATOM 3 C4' DC A 1 17.780 12.428 4.683 1.00 5.43 C ATOM 4 O4' DC A 1 16.900 13.637 5.169 1.00 6.23 O ATOM 5 C3' DC A 1 16.903 11.517 3.475 1.00 5.76 C ATOM 6 O3' DC A 1 16.848 10.473 4.192 1.00 6.24 O ATOM 7 C2' DC A 1 15.977 12.516 3.163 1.00 5.97 C ATOM 8 C1' DC A 1 15.473 13.380 4.327 1.00 5.80 C ATOM 9 N1 DC A 1 14.721 14.504 4.148 1.00 5.86 N ATOM 10 C2 DC A 1 13.295 14.451 4.290 1.00 5.95 C ATOM 11 O2 DC A 1 12.608 13.668 4.294 1.00 7.16 O ATOM 12 N3 DC A 1 12.794 15.674 3.726 1.00 5.87 N ATOM 13 C4 DC A 1 13.623 16.916 3.582 1.00 5.87 C ATOM 14 N4 DC A 1 12.698 18.168 3.295 1.00 6.52 N ATOM 15 C5 DC A 1 15.075 16.801 3.752 1.00 6.61 C ATOM 16 C6 DC A 1 15.640 15.653 3.819 1.00 6.96 C ATOM 17 P DG A 2 17.631 9.187 3.781 1.00 6.42 P ATOM 18 OP1 DG A 2 18.530 9.316 2.435 1.00 7.41 O ATOM 19 OP2 DG A 2 16.668 7.990 3.994 1.00 7.63 O ATOM 20 O5' DG A 2 18.419 9.169 5.189 1.00 6.87 O ATOM 21 C5' DG A 2 18.197 9.223 6.308 1.00 6.28 C ATOM 22 C4' DG A 2 19.205 9.558 7.462 1.00 6.57 C ATOM 23 O4' DG A 2 19.611 10.643 7.367 1.00 6.18 O ATOM 24 C3' DG A 2 18.893 9.465 8.720 1.00 6.90 C ATOM 25 O3' DG A 2 18.617 7.901 9.449 1.00 8.35 O ATOM 26 C2' DG A 2 19.721 10.190 9.807 1.00 7.77 C ATOM 27 C1' DG A 2 20.006 11.229 8.414 1.00 6.65 C ATOM 28 N9 DG A 2 19.144 12.823 8.744 1.00 6.28 N ATOM 29 C8 DG A 2 19.751 13.993 9.106 1.00 7.19 C ATOM 30 N7 DG A 2 19.167 14.955 9.254 1.00 7.47 N ATOM 31 C5 DG A 2 17.619 14.462 8.993 1.00 5.84 C ATOM 32 C6 DG A 2 16.547 14.971 8.491 1.00 5.59 C ATOM 33 O6 DG A 2 16.216 16.020 8.843 1.00 6.73 O ATOM 34 N1 DG A 2 15.417 14.114 8.033 1.00 5.14 N ATOM 35 C2 DG A 2 16.031 12.765 7.873 1.00 4.97 C ATOM 36 N2 DG A 2 14.640 11.946 7.438 1.00 5.85 N ATOM 37 N3 DG A 2 17.153 11.919 8.147 1.00 5.27 N ATOM 38 C4 DG A 2 17.851 13.132 8.324 1.00 5.60 C ATOM 39 P DC A 3 17.502 7.309 9.844 1.00 8.32 P ATOM 40 OP1 DC A 3 17.951 5.867 10.049 1.00 10.45 O ATOM 41 OP2 DC A 3 16.550 7.398 9.077 1.00 9.29 O ATOM 42 O5' DC A 3 17.323 8.078 11.161 1.00 7.83 O ATOM 43 C5' DC A 3 16.537 7.185 12.484 1.00 6.84 C ATOM 44 C4' DC A 3 15.368 7.829 12.973 1.00 6.76 C ATOM 45 O4' DC A 3 15.906 9.208 13.536 1.00 6.82 O ATOM 46 C3' DC A 3 14.080 8.010 11.984 1.00 7.23 C ATOM 47 O3' DC A 3 12.932 8.214 12.827 1.00 8.29 O ATOM 48 C2' DC A 3 14.502 9.696 11.586 1.00 7.01 C ATOM 49 C1' DC A 3 15.121 10.054 12.879 1.00 6.65 C ATOM 50 N1 DC A 3 15.870 11.674 12.436 1.00 6.27 N ATOM 51 C2 DC A 3 15.272 12.628 12.764 1.00 6.39 C ATOM 52 O2 DC A 3 13.887 12.738 13.262 1.00 6.84 O ATOM 53 N3 DC A 3 15.949 13.828 12.480 1.00 6.04 N ATOM 54 C4 DC A 3 17.047 13.736 12.007 1.00 6.43 C ATOM 55 N4 DC A 3 17.968 14.885 11.886 1.00 7.42 N ATOM 56 C5 DC A 3 17.840 12.301 12.086 1.00 7.12 C ATOM 57 C6 DC A 3 17.186 11.363 12.180 1.00 6.73 C ATOM 58 P DG A 4 12.004 6.579 12.593 1.00 9.26 P ATOM 59 OP1 DG A 4 12.160 6.144 11.154 1.00 12.46 O ATOM 60 OP2 DG A 4 11.035 6.669 13.355 1.00 14.73 O ATOM 61 O5' DG A 4 13.064 5.660 13.726 1.00 7.56 O ATOM 62 C5' DG A 4 12.931 5.750 14.924 1.00 6.32 C ATOM 63 C4' DG A 4 13.949 4.733 15.512 1.00 5.92 C ATOM 64 O4' DG A 4 15.498 5.413 15.267 1.00 5.78 O ATOM 65 C3' DG A 4 14.171 4.708 17.252 1.00 5.01 C ATOM 66 O3' DG A 4 13.508 3.987 17.712 1.00 5.69 O ATOM 67 C2' DG A 4 15.823 4.484 17.315 1.00 6.12 C ATOM 68 C1' DG A 4 16.551 4.971 16.232 1.00 5.65 C ATOM 69 N9 DG A 4 17.292 6.386 16.378 1.00 5.85 N ATOM 70 C8 DG A 4 18.506 6.600 16.684 1.00 7.25 C ATOM 71 N7 DG A 4 18.815 7.882 16.775 1.00 7.01 N ATOM 72 C5 DG A 4 17.566 8.317 16.955 1.00 5.60 C ATOM 73 C6 DG A 4 17.372 9.788 16.816 1.00 5.58 C ATOM 74 O6 DG A 4 18.199 10.657 17.123 1.00 6.97 O ATOM 75 N1 DG A 4 16.188 10.185 16.558 1.00 5.26 N ATOM 76 C2 DG A 4 14.888 9.117 16.295 1.00 4.93 C ATOM 77 N2 DG A 4 13.978 9.590 16.453 1.00 5.47 N ATOM 78 N3 DG A 4 15.451 7.903 16.321 1.00 5.01 N ATOM 79 C4 DG A 4 16.459 7.404 16.414 1.00 5.12 C ATOM 80 P DC A 5 12.772 3.902 19.038 1.00 5.45 P ATOM 81 OP1 DC A 5 14.279 3.981 20.147 1.00 7.21 O ATOM 82 OP2 DC A 5 11.998 2.997 19.367 1.00 6.66 O ATOM 83 O5' DC A 5 12.022 5.431 19.103 1.00 5.28 O ATOM 84 C5' DC A 5 11.334 5.544 20.249 1.00 4.67 C ATOM 85 C4' DC A 5 10.943 7.022 20.772 1.00 4.60 C ATOM 86 O4' DC A 5 12.405 7.639 21.156 1.00 4.74 O ATOM 87 C3' DC A 5 10.518 7.796 19.459 1.00 4.77 C ATOM 88 O3' DC A 5 9.551 8.904 19.516 1.00 5.08 O ATOM 89 C2' DC A 5 11.807 8.652 18.820 1.00 4.62 C ATOM 90 C1' DC A 5 12.744 8.983 20.111 1.00 4.39 C ATOM 91 N1 DC A 5 13.937 8.968 20.325 1.00 4.58 N ATOM 92 C2 DC A 5 14.614 10.225 20.025 1.00 4.24 C ATOM 93 O2 DC A 5 13.934 11.123 20.012 1.00 4.74 O ATOM 94 N3 DC A 5 15.926 10.008 19.965 1.00 4.45 N ATOM 95 C4 DC A 5 16.974 9.239 20.013 1.00 4.35 C ATOM 96 N4 DC A 5 18.063 9.323 19.960 1.00 5.02 N ATOM 97 C5 DC A 5 16.378 7.834 20.137 1.00 5.31 C ATOM 98 C6 DC A 5 14.775 7.783 20.156 1.00 4.82 C ATOM 99 P DG A 6 8.103 8.716 19.351 1.00 5.08 P ATOM 100 OP1 DG A 6 8.308 7.937 17.755 1.00 6.02 O ATOM 101 OP2 DG A 6 7.257 10.030 19.470 1.00 6.23 O ATOM 102 O5' DG A 6 7.627 7.422 20.259 1.00 5.07 O ATOM 103 C5' DG A 6 7.203 7.790 21.297 1.00 5.27 C ATOM 104 C4' DG A 6 6.972 6.647 22.158 1.00 5.46 C ATOM 105 O4' DG A 6 8.258 6.009 22.883 1.00 5.73 O ATOM 106 C3' DG A 6 6.097 6.940 23.542 1.00 5.95 C ATOM 107 O3' DG A 6 5.267 5.980 23.696 1.00 6.71 O ATOM 108 C2' DG A 6 7.077 7.060 24.603 1.00 5.78 C ATOM 109 C1' DG A 6 8.105 6.138 24.281 1.00 5.71 C ATOM 110 N9 DG A 6 9.592 6.377 24.627 1.00 5.53 N ATOM 111 C8 DG A 6 10.207 5.269 25.424 1.00 6.04 C ATOM 112 N7 DG A 6 11.421 5.902 25.774 1.00 6.08 N ATOM 113 C5 DG A 6 11.524 7.174 24.874 1.00 5.46 C ATOM 114 C6 DG A 6 12.666 8.150 24.715 1.00 5.43 C ATOM 115 O6 DG A 6 13.806 7.876 25.335 1.00 7.16 O ATOM 116 N1 DG A 6 12.202 9.109 23.974 1.00 4.97 N ATOM 117 C2 DG A 6 10.786 9.275 23.280 1.00 4.93 C ATOM 118 N2 DG A 6 10.584 10.385 22.676 1.00 5.51 N ATOM 119 N3 DG A 6 9.936 8.281 23.715 1.00 5.24 N ATOM 120 C4 DG A 6 10.352 7.374 24.191 1.00 5.04 C TER ATOM 121 O5' DC B 11 18.390 16.178 25.020 1.00 8.02 O ATOM 122 C5' DC B 11 17.802 16.563 23.727 1.00 6.88 C ATOM 123 C4' DC B 11 16.475 16.367 23.351 1.00 5.81 C ATOM 124 O4' DC B 11 16.581 14.886 23.292 1.00 5.58 O ATOM 125 C3' DC B 11 15.567 16.424 24.589 1.00 5.79 C ATOM 126 O3' DC B 11 14.388 17.157 24.214 1.00 5.67 O ATOM 127 C2' DC B 11 15.358 15.062 25.107 1.00 5.97 C ATOM 128 C1' DC B 11 15.362 14.168 23.911 1.00 5.24 C ATOM 129 N1 DC B 11 16.072 12.794 24.216 1.00 5.01 N ATOM 130 C2 DC B 11 14.969 11.784 24.351 1.00 4.82 C ATOM 131 O2 DC B 11 14.004 12.120 23.953 1.00 5.52 O ATOM 132 N3 DC B 11 15.575 10.519 24.617 1.00 4.74 N ATOM 133 C4 DC B 11 16.648 10.434 24.558 1.00 4.81 C ATOM 134 N4 DC B 11 17.263 9.089 24.737 1.00 5.77 N ATOM 135 C5 DC B 11 17.799 11.390 24.582 1.00 5.27 C ATOM 136 C6 DC B 11 17.277 12.685 24.472 1.00 5.27 C ATOM 137 P DG B 12 14.063 18.580 24.253 1.00 5.73 P ATOM 138 OP1 DG B 12 14.515 19.155 25.429 1.00 7.08 O ATOM 139 OP2 DG B 12 12.595 18.913 23.977 1.00 6.80 O ATOM 140 O5' DG B 12 14.862 19.150 23.008 1.00 5.63 O ATOM 141 C5' DG B 12 14.356 18.875 21.718 1.00 5.55 C ATOM 142 C4' DG B 12 15.395 19.631 20.531 1.00 5.48 C ATOM 143 O4' DG B 12 16.373 18.884 20.689 1.00 5.59 O ATOM 144 C3' DG B 12 14.685 19.238 19.167 1.00 5.35 C ATOM 145 O3' DG B 12 13.921 20.367 18.684 1.00 5.75 O ATOM 146 C2' DG B 12 16.395 19.357 18.328 1.00 6.20 C ATOM 147 C1' DG B 12 17.393 19.037 19.623 1.00 5.70 C ATOM 148 N9 DG B 12 17.756 17.291 19.447 1.00 5.43 N ATOM 149 C8 DG B 12 19.095 16.934 18.862 1.00 6.29 C ATOM 150 N7 DG B 12 19.008 15.920 18.711 1.00 6.25 N ATOM 151 C5 DG B 12 17.723 15.302 19.321 1.00 5.07 C ATOM 152 C6 DG B 12 17.465 14.049 19.481 1.00 5.05 C ATOM 153 O6 DG B 12 18.109 12.934 19.018 1.00 6.39 O ATOM 154 N1 DG B 12 16.159 13.768 19.730 1.00 4.49 N ATOM 155 C2 DG B 12 15.334 15.147 20.261 1.00 4.50 C ATOM 156 N2 DG B 12 14.217 14.760 20.752 1.00 5.39 N ATOM 157 N3 DG B 12 15.746 16.198 20.052 1.00 4.99 N ATOM 158 C4 DG B 12 17.074 16.421 19.555 1.00 4.82 C ATOM 159 P DC B 13 12.678 19.767 18.152 1.00 5.23 P ATOM 160 OP1 DC B 13 11.869 20.815 17.883 1.00 6.06 O ATOM 161 OP2 DC B 13 11.982 18.700 19.291 1.00 6.16 O ATOM 162 O5' DC B 13 12.924 18.779 16.938 1.00 6.62 O ATOM 163 C5' DC B 13 11.685 18.678 16.017 1.00 5.76 C ATOM 164 C4' DC B 13 11.180 17.477 15.593 1.00 5.29 C ATOM 165 O4' DC B 13 12.554 16.556 15.013 1.00 5.84 O ATOM 166 C3' DC B 13 10.859 16.392 16.854 1.00 5.51 C ATOM 167 O3' DC B 13 9.785 15.914 16.816 1.00 5.91 O ATOM 168 C2' DC B 13 11.948 15.746 17.260 1.00 6.03 C ATOM 169 C1' DC B 13 12.840 15.319 16.034 1.00 5.71 C ATOM 170 N1 DC B 13 14.237 15.100 16.204 1.00 5.35 N ATOM 171 C2 DC B 13 14.431 13.844 16.104 1.00 5.14 C ATOM 172 O2 DC B 13 13.785 12.841 16.376 1.00 5.75 O ATOM 173 N3 DC B 13 15.731 13.493 16.249 1.00 5.24 N ATOM 174 C4 DC B 13 16.753 14.441 16.224 1.00 5.38 C ATOM 175 N4 DC B 13 17.895 14.264 16.090 1.00 6.48 N ATOM 176 C5 DC B 13 16.199 15.736 16.104 1.00 6.18 C ATOM 177 C6 DC B 13 15.162 15.939 16.120 1.00 5.88 C ATOM 178 P DG B 14 8.272 16.421 16.796 1.00 6.36 P ATOM 179 OP1 DG B 14 8.360 16.932 18.219 1.00 6.92 O ATOM 180 OP2 DG B 14 7.245 14.971 16.815 1.00 8.20 O ATOM 181 O5' DG B 14 8.088 17.461 15.506 1.00 6.06 O ATOM 182 C5' DG B 14 8.027 16.856 14.427 1.00 5.87 C ATOM 183 C4' DG B 14 7.697 17.989 13.192 1.00 5.61 C ATOM 184 O4' DG B 14 9.260 18.737 13.333 1.00 6.39 O ATOM 185 C3' DG B 14 7.733 17.338 11.903 1.00 6.20 C ATOM 186 O3' DG B 14 6.494 17.192 11.417 1.00 6.92 O ATOM 187 C2' DG B 14 8.302 18.895 11.265 1.00 6.66 C ATOM 188 C1' DG B 14 9.437 19.067 12.135 1.00 6.45 C ATOM 189 N9 DG B 14 10.701 19.070 11.753 1.00 5.88 N ATOM 190 C8 DG B 14 11.918 19.990 11.280 1.00 6.66 C ATOM 191 N7 DG B 14 12.868 19.546 11.476 1.00 6.84 N ATOM 192 C5 DG B 14 12.649 18.022 11.679 1.00 5.83 C ATOM 193 C6 DG B 14 13.602 17.047 11.491 1.00 5.83 C ATOM 194 O6 DG B 14 14.927 16.875 11.151 1.00 7.03 O ATOM 195 N1 DG B 14 13.042 15.748 12.041 1.00 5.52 N ATOM 196 C2 DG B 14 11.672 15.592 12.236 1.00 5.22 C ATOM 197 N2 DG B 14 11.348 14.455 12.712 1.00 5.90 N ATOM 198 N3 DG B 14 10.836 16.766 12.350 1.00 5.73 N ATOM 199 C4 DG B 14 11.354 17.756 12.028 1.00 5.44 C ATOM 200 P DC B 15 6.218 15.986 10.586 1.00 7.01 P ATOM 201 OP1 DC B 15 4.510 15.946 10.477 1.00 8.31 O ATOM 202 OP2 DC B 15 6.747 14.887 11.105 1.00 10.11 O ATOM 203 O5' DC B 15 6.697 16.141 9.256 1.00 8.26 O ATOM 204 C5' DC B 15 6.431 15.640 7.947 1.00 6.44 C ATOM 205 C4' DC B 15 7.332 14.796 7.485 1.00 6.19 C ATOM 206 O4' DC B 15 8.887 15.306 7.140 1.00 6.22 O ATOM 207 C3' DC B 15 7.729 13.783 8.602 1.00 6.74 C ATOM 208 O3' DC B 15 7.849 12.490 7.866 1.00 7.06 O ATOM 209 C2' DC B 15 9.421 14.123 9.032 1.00 7.26 C ATOM 210 C1' DC B 15 9.994 14.685 7.840 1.00 6.21 C ATOM 211 N1 DC B 15 10.816 15.849 8.023 1.00 5.66 N ATOM 212 C2 DC B 15 12.121 15.204 7.903 1.00 5.46 C ATOM 213 O2 DC B 15 12.294 13.987 7.871 1.00 6.74 O ATOM 214 N3 DC B 15 13.411 16.017 8.254 1.00 5.33 N ATOM 215 C4 DC B 15 12.697 17.294 8.452 1.00 5.54 C ATOM 216 N4 DC B 15 14.005 18.139 8.707 1.00 6.29 N ATOM 217 C5 DC B 15 11.616 18.009 8.496 1.00 6.28 C ATOM 218 C6 DC B 15 10.506 16.956 7.950 1.00 5.99 C ATOM 219 P DG B 16 6.746 11.289 8.146 1.00 7.56 P ATOM 220 OP1 DG B 16 6.487 11.279 9.874 1.00 9.30 O ATOM 221 OP2 DG B 16 7.228 10.074 7.851 1.00 10.00 O ATOM 222 O5' DG B 16 5.638 11.663 7.331 1.00 6.99 O ATOM 223 C5' DG B 16 5.337 11.421 6.141 1.00 6.54 C ATOM 224 C4' DG B 16 4.283 12.081 5.287 1.00 5.93 C ATOM 225 O4' DG B 16 4.658 13.293 5.164 1.00 5.90 O ATOM 226 C3' DG B 16 3.864 11.520 4.009 1.00 6.25 C ATOM 227 O3' DG B 16 2.393 11.576 4.196 1.00 6.18 O ATOM 228 C2' DG B 16 4.623 12.031 2.975 1.00 6.00 C ATOM 229 C1' DG B 16 4.307 13.500 3.878 1.00 5.55 C ATOM 230 N9 DG B 16 5.591 14.582 3.394 1.00 5.41 N ATOM 231 C8 DG B 16 5.456 15.603 2.606 1.00 5.68 C ATOM 232 N7 DG B 16 6.305 16.450 2.616 1.00 6.51 N ATOM 233 C5 DG B 16 7.431 15.552 3.086 1.00 5.15 C ATOM 234 C6 DG B 16 8.756 15.541 2.915 1.00 5.40 C ATOM 235 O6 DG B 16 9.537 16.295 2.806 1.00 6.71 O ATOM 236 N1 DG B 16 9.587 14.409 3.788 1.00 5.34 N ATOM 237 C2 DG B 16 8.585 13.432 4.167 1.00 4.88 C ATOM 238 N2 DG B 16 9.598 12.532 4.976 1.00 6.11 N ATOM 239 N3 DG B 16 7.242 13.447 4.092 1.00 5.45 N ATOM 240 C4 DG B 16 6.936 14.354 3.721 1.00 5.38 C TER """ def get_pdb_inputs(pdb_str, restraints): ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files( raw_records=pdb_str.splitlines())[0] xrs = ppf.xray_structure(show_summary = False) restraints_manager=None if(restraints): restraints_manager = mmtbx.restraints.manager( geometry = ppf.geometry_restraints_manager(show_energies = False), normalization = True) return group_args( ph = ppf.all_chain_proxies.pdb_hierarchy, grm = restraints_manager, xrs = xrs) def get_map(xrs): f_calc = xrs.structure_factors(d_min = 1.2).f_calc() fft_map = f_calc.fft_map(resolution_factor=0.25) fft_map.apply_sigma_scaling() return fft_map.real_map_unpadded() def exercise(): """ Exercise refine "easy" with DNA/RNA. """ pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False) map_data = get_map(xrs=pi_good.xrs) xrs_good = pi_good.xrs.deep_copy_scatterers() pi_good.ph.write_pdb_file(file_name="answer.pdb", crystal_symmetry=xrs_good.crystal_symmetry()) # pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True) pi_poor.ph.write_pdb_file(file_name="poor.pdb") xrs_poor = pi_poor.xrs.deep_copy_scatterers() # d = xrs_good.distances(other=xrs_poor) print(d.min_max_mean().as_tuple()) assert flex.max(d)>2 assert flex.mean(d)>0.7 # xrs_refined = xrs_poor for i in range(3): ero = individual_sites.easy( map_data = map_data, xray_structure = xrs_refined, pdb_hierarchy = pi_poor.ph, geometry_restraints_manager = pi_poor.grm) xrs_refined = ero.xray_structure # comapre d = xrs_good.distances(other=xrs_refined) print(d.min_max_mean().as_tuple()) assert flex.max(d)<0.15 assert flex.mean(d)<0.03 ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb", crystal_symmetry=xrs_good.crystal_symmetry()) if(__name__ == "__main__"): timer = user_plus_sys_time() exercise() print("Time: %6.2f" % timer.elapsed()) print("OK")